Freesurfer

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30070 discussions

Re: [Freesurfer] Freesurfer binary for Centos 9
by fsbuild 21 Jun '23

21 Jun '23

External Email - Use Caution I would suggest someone try installing the CentOS8 RPM file and if that succeeds, then you could try running freesurfer.   However, freesurfer has not been tested running on “CentOS9 stream” or the current RHEL 9 release and I would not expect it to build natively there.   We are looking at what OS’s should be supported and will consider your request. - R. On Jun 21, 2023, at 05:05, Knut J Bjuland <knutjorgen(a)outlook.com> wrote:        External Email - Use Caution        Dear Freesurfer surfer experts,Will Freesurfer surfer be built for Centos 9 as the cluster I am using has now been upgraded to Centos 9? Is there a source package for Freesurfer 7.4.1?Best regards, Knut Jørgen Bjuland _______________________________________________Freesurfer mailing listFreesurfer@nmr..mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Vbox password
by neda_afzalian 21 Jun '23

21 Jun '23

External Email - Use Caution Would you please send me the unzip pass for freesurfer again? The last one did not work

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Inconsistent number of ROIs in ?.aparc.DKTatlas.stats
by Karoui, Hajer 21 Jun '23

21 Jun '23

External Email - Use Caution Hello, I am running into a major issue when I run recon-all -all on the OASIS1 cohort. I am getting an inconsistent number of ROIs for the same subject between the lh and rh, resulting in different sizes of connectivity matrices across subjects (various numbers of ROIs {27, 28, 29, 30, 31,32}. For all subjects from other cohorts, patients and controls, it was 31 ROIs). I tried inspecting which ROIs usually cause this difference between the two hemispheres, it differs from subject to subject, but here is a comprehensive list of all the problematic ROIs that came up. Please not this is a cohort of healthy controls this issue is coming up for. I ran this on a set of patients with Multiple Sclerosis, and I got a consistent number of 31 ROIs. {'insula', 'parahippocampal', 'caudalmiddlefrontal', 'parsorbitalis', 'paracentral', 'transversetemporal', 'parsopercularis', 'superiortemporal', 'postcentral', 'isthmuscingulate', 'inferiortemporal', 'superiorparietal', 'parstriangularis', 'middletemporal', 'rostralanteriorcingulate', 'lateraloccipital', 'entorhinal', 'posteriorcingulate', 'lingual', 'pericalcarine', 'inferiorparietal', 'precentral', 'cuneus', 'fusiform', 'lateralorbitofrontal', 'caudalanteriorcingulate', 'superiorfrontal', 'medialorbitofrontal', 'precuneus', 'supramarginal', 'temporalpole', 'rostralmiddlefrontal'} Any idea what this might be due to? This is quite a big issue for our pipeline so any help would be appreciated. Thanks, and looking forward to your response. Hajer Karoui Data Manager & Researcher | MS & PD Tissue Bank Imperial College London Department of Brain Sciences LinkedIn<https://secure-web.cisco.com/1OeYrjhIt9Fk085_UN6qcwoS-MNLucvE34f-51vAnmxH5x…> [cid:4345924b-28e1-4b07-947d-e7b515fc02ea]

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Inconsistent number of ROIs in ?.aparc.DKTatlas.stats
by Karoui, Hajer 21 Jun '23

21 Jun '23

External Email - Use Caution Hello, I hope my email finds you well. I am running into a major issue when I run recon-all -all on the OASIS1 cohort. I am getting an inconsistent number of ROIs for the same subject between the lh and rh, resulting in different sizes of connectivity matrices across subjects (various numbers of ROIs {27, 28, 29, 30, 31,32}. For all subjects from other cohorts, patients and controls, it was 31 ROIs). Please find below a quick example, subject OAS1_0384 is fine, whereas OAS1_0167 and OAS1_0159 are not. [cid:ab6e09d5-0731-49fd-8841-b7f1c6c698e8] I tried inspecting which ROIs usually cause this difference between the two hemispheres, it differs from subject to subject, but here is a comprehensive list of all the problematic ROIs that came up. Please not this is a cohort of healthy controls this issue is coming up for. I ran this on a set of patients with Multiple Sclerosis, and I got a consistent number of 31 ROIs. {'insula', 'parahippocampal', 'caudalmiddlefrontal', 'parsorbitalis', 'paracentral', 'transversetemporal', 'parsopercularis', 'superiortemporal', 'postcentral', 'isthmuscingulate', 'inferiortemporal', 'superiorparietal', 'parstriangularis', 'middletemporal', 'rostralanteriorcingulate', 'lateraloccipital', 'entorhinal', 'posteriorcingulate', 'lingual', 'pericalcarine', 'inferiorparietal', 'precentral', 'cuneus', 'fusiform', 'lateralorbitofrontal', 'caudalanteriorcingulate', 'superiorfrontal', 'medialorbitofrontal', 'precuneus', 'supramarginal', 'temporalpole', 'rostralmiddlefrontal'} I attached a few examples. Any idea what this might be due to? This is quite a big issue for our pipeline so any help would be appreciated. Thanks, and looking forward to your response. Hajer Karoui Data Manager & Researcher | MS & PD Tissue Bank Imperial College London Department of Brain Sciences LinkedIn<https://secure-web.cisco.com/1JO7xNCIyxfajee8Ev2WuUyu6FQChzXcn1tXpNtESmlpj8…> [cid:5bdd6a0d-136c-4240-862a-c9df55fc7797]

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request for password
by Yifei Fan 21 Jun '23

21 Jun '23

External Email - Use Caution Dear freesurfer, I'm a medical physics student at the University of Manchester, I just downloaded the FS_7_2_0_ubuntu_18_04_06.ova.7z on my mac computer. please send me a password. Best, Yifei

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Pass code Request
by Freya Bowden 21 Jun '23

21 Jun '23

External Email - Use Caution Hello, I am installing Freesurfer on a Windows 10 device and I have been asked for a passcode to open the 7z file. Please can I request this? Thank you, Freya

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Freesurfer binary for Centos 9
by Knut J Bjuland 21 Jun '23

21 Jun '23

External Email - Use Caution Dear Freesurfer surfer experts, Will Freesurfer surfer be built for Centos 9 as the cluster I am using has now been upgraded to Centos 9? Is there a source package for Freesurfer 7.4.1? Best regards, Knut Jørgen Bjuland

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recon-all-clinical
by Andrew Dedinas Geoly 20 Jun '23

20 Jun '23

External Email - Use Caution Hello Freesurfer experts! I am conducting a longitudinal GMV and CT analysis of mTBI participants who received an experimental single-dose pharmacological treatment. We collected GE Bravo (0.9mm isotropic) T1w data pre, immediately after (~ 4 days after intervention) and 1-month following the intervention. I have been working with the recon-all longitudinal pipeline stream (7.1.1) but have noticed pretty significant errors in terms of skull stripping and segmentation (participants are veterans with somewhat random lesion / atrophy patterns). I have tested your new recon-all-clinical program (7.4.0) on some of my worst cases and it is performing remarkably well. I am doing some more digging into the various synth segmentation packages available in FS newest versions and was wondering what the best course of action would be for integrating recon-all-clinical or synthseg into a longitudinal workflow. 1.Could I use the recon-all-clinical outputs as the "cross" for later base and long template construction? 2. SynthSeg and SCLimbic seem to have very good test-retest reliability-- would it be feasible to use the independent segmentation extractions from those and bypass the longitudinal stream entirely (not saying I would want to but I am curious)? Any and all help here would be greatly appreciated, and I thank you very much for your time. Warmest regards, Andrew --- Andrew D. Geoly, MS Research Data Analyst 1 Brain Stimulation Lab Department of Psychiatry and Behavioral Sciences Stanford University School of Medicine

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FS 7.4.1, MiDeFace fix
by Douglas N. Greve 20 Jun '23

20 Jun '23

External Email - Use Caution FS 7.4.1 is now available here https://secure-web.cisco.com/17-PRJfqpn9BuagsDlTJ1iBDfnqh2fW4JB_SRTk0Nrzd56… The only change is a bug fix to MiDeFace. https://secure-web.cisco.com/1InRJsRxr1cJyXEd0j0nFXhSVxdktDhalS8LTSCvY-rSOK… A bug was found in the 7.4.0 version of MiDeFace when creating the head mask and true face surface. In a small number of cases, it was found that the thresholds were being set too high causing an undersegmentation of the head. The problem was worse in non-T1w contrasts. This likely does not compromise privacy; rather, it typically caused the defacing to be too aggressive. Release notes are here https://secure-web.cisco.com/1gJhtPWK_PcnfeYYEH5vaPwUgai85exNagU7tYLZl_yPeK… thanks and sorry for any inconvenience doug

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How are they using freesurfer in a big dataset?
by Michelle Diniz 20 Jun '23

20 Jun '23

External Email - Use Caution Hey guys. I'm using FMRIprep on the OASIS3 database and I've noticed that the processing time for each subject averages two days. 80% of that processing is due to the freesurfer. I will need to analyze many resonance images, more precisely the functional part. I tested SMRIprep and didn't get a significant improvement in processing time. How are you getting around this type of problem? How are they using freesurfer in a big dataset? -- Michelle Diniz Lopes

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